We present a general analytic method for understanding how specific motions of a classical bath influence the dynamics of quantum mechanical observables in mixed quantum/classical molecular dynamics simulations. We apply our method and develop expressions for the special case of quantum solvation, allowing us to examine how specific classical solvent motions couple to the equilibrium energy flu...

a multiple linear regression model is proposed to calculate capacity factor of  analytes using structural features computed using hyperchem software. the  chemical descriptors of analytes were computed using hyperchem software and  regressed against the experimental capacity factors of analytes collected from the  literature. the absolute average percentage deviation (aard) and individual perce...

Simplified models and empirical potentials are being increasingly used for the analysis of proteins, frequently augmenting or replacing molecular mechanics approaches. Recent folding simulations have employed potentials that, in addition to terms assuring proper polypeptide geometry, include only two noncovalent effects-hydrogen bonding and hydrophobicity, with extremely simple approximations t...

We include solvation effects in tight-binding Hamiltonians for hole states in DNA. The corresponding linear-response parameters are derived from accurate estimates of solvation energy calculated for several hole charge distributions in DNA stacks. Two models are considered: (A) the correction to a diagonal Hamiltonian matrix element depends only on the charge localized on the corresponding site...

The SAMPL2 hydration free energy blind prediction challenge consisted of a data set of 41 molecules divided into three subsets: explanatory, obscure and investigatory, where experimental hydration free energies were given for the explanatory, withheld for the obscure, and not known for the investigatory molecules. We employed two solvation models for this challenge, a linear interaction energy ...

A validation based on solvation energies (vacuum to water transfer) is not sufficient to justify the use of approximated models of electrostatics to rank ligand/protein complexes. A full validation should be based on energies in solution, i.e., solvation plus vacuum Coulomb energies, because of the anticorrelation between solvation and vacuum energies. The energy in solution is the relevant qua...

Quantum mechanical calculations of different energies components of 1,10-phenanthroline in ground state were carried out by DFT method , in isolated state and in various solvents to study the effects of solvents on various energy components and global properties. The solvation energy, chemical potential, hardness, electrophilicity of 1,10-phenanthroline were calculated with the help of computed...

A method is developed to include solvation effects in linear-scaling semiempirical quantum calculations. Favorable scaling of computational effort for large molecules is achieved using a preconditioned conjugate gradient technique in conjunction with a linear-scaling recursive bisection method for evaluation of electrostatic interactions. The method requires approximately 30% computational over...

A fast method for the calculation of residue contributions to protein solvation is presented. The approach uses the exposed polar and apolar surface of protein residues and has been parametrized from the fractional contributions to solvation determined from linear response theory coupled to molecular dynamics simulations. Application of the method to a large subset of proteins taken from the Pr...

We present a new methodology for computing solvation free energy, which is based upon the reference interaction site model (RISM)/hypernetted chain (HNC) solvation free energy expression, but which substitutes radial distribution functions taken from simulations for those calculated by simultaneous solution of the RISM and HNC equations. Consequently, solvation free energy can be obtained from ...